L. Fumagalli's research while affiliated with University of Lausanne and other places

Publications (255)

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Assessing the diet of wild animals reveals valuable information about their ecology and trophic relationships that may help elucidate dynamic interactions in ecosystems and forecast responses to environmental changes. Advances in molecular biology provide valuable research tools in this field. However, comparative empirical research is still requir...
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Biodiversity assessments are indispensable tools for planning and monitoring conservation strategies. Camera traps (CT) are widely used to monitor wildlife and have proven their usefulness. Environmental DNA (eDNA)-based approaches are increasingly implemented for biomonitoring, combining sensitivity, high taxonomic coverage and resolution, non-inv...
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Significance Reproductive isolation is instrumental to the formation of new species (speciation), but it remains largely enigmatic how many incompatibilities are required to prevent hybridization and where they lie across the genome. By studying patterns of admixture in amphibian hybrid zones, we found that reproductive isolation is initiated by nu...
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Cannabis sativa has long been an important source of fiber extracted from hemp and both medicinal and recreational drugs based on cannabinoid compounds. Here, we investigated its poorly known domestication history using whole-genome resequencing of 110 accessions from worldwide origins. We show that C. sativa was first domesticated in early Neolith...
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Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. While the identification of food components of plant and animal origin has traditionally been conducted by macro- and microscopical approaches in case of incomplete digestion, molecular methods provide the potential to increase sensitivity and tax...
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Delineating population boundaries in anthropogenic landscape is of critical importance for domains of biology that are concerned with the ecology, evolution and conservation of species. This remains particularly difficult for species where there is no obvious demarcation of geographical populations and dispersal patterns are poorly known. This is o...
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The return of top carnivores to their historical range triggers conflicts with the interests of different stakeholder groups. Anticipating such conflicts is key to appropriate conservation management, which calls for reliable spatial predictions of future carnivore occurrence. Previous models have assessed general habitat suitability for wolves, bu...
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Molecular ecologists often rely on phylogenetic evidence for assessing the species-level systematics of newly-discovered lineages. Alternatively, the extent of introgression at phylogeographic transitions can provide a more direct test to assign candidate taxa into subspecies or species categories. Here we compared phylogenetic versus hybrid zone a...
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Disentangling the sources of variation in developing an effective immune response against pathogens is of major interest to immunoecology and evolutionary biology. To date, the link between immunocompetence and genetic variation at the major histocompatibility complex (MHC) has received little attention in wild animals, despite the key role of MHC...
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The sociopolitical acceptance necessary for the conservation of controversial species requires scientific knowledge that disentangles empirical facts from myth and misinformation. An epitome of such, the grey wolf (Canis lupus), had been eradicated from most of Western Europe by the early 20th century. However, a few mysteriously re-appeared in the...
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Rapid management responses against invasive species soon after their establishment is the most efficient way to limit their biological and economic impacts. Early-detection and reliable monitoring is however challenging when cryptic taxa are involved. Here we show how environmental DNA (eDNA) metabarcoding of water samples efficiently unveiled an e...
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Comparative molecular studies emphasized a new biogeographic paradigm for the terrestrial fauna of North Africa, one of the last uncharted ecoregions of the Western Palearctic: two independent east-west divisions across the Maghreb. Through a comprehensive phylogeography, we assessed how this model suits the genetic diversification documented for t...
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Potential hybridization between wolves and dogs has fueled the sensitive conservation and political debate underlying the recovery of the grey wolf throughout Europe. Here we provide the first genetic analysis of wolf-dog admixture in an area entirely recolonized, the northwestern Alps. As part of a long-term monitoring program, we performed geneti...
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Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) makes an iconic example of extreme declines driven by anthropogenic factors. Here we assessed the genetic signatures of 150 years of wolf persecution throughout the Western...
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High rates of gene duplication and the highest levels of functional allelic diversity in vertebrate genomes are the main hallmarks of the major histocompatibility complex (MHC), a multigene family with a primordial role in pathogen recognition. The usual tight linkage among MHC gene duplicates may provide an opportunity for the evolution of haploty...
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Background Gene duplication has led to a most remarkable adaptation involved in vertebrates’ host-pathogen arms-race, the major histocompatibility complex (MHC). However, MHC duplication history is as yet poorly understood in non-mammalian vertebrates, including birds. Results Here, we provide evidence for the evolution of two ancient avian MHC cl...
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Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The im...
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Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breedin...
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Tree of genetic distances (pairwise Fst) between Cannabis accessions. Monoecious hemp are highlighted in grey. (TIF)
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Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties base...
Data
Genetic structure among marijuana samples. (TIF)
Data
List and details on the Cannabis accessions. (XLSX)
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Characterization of 106 polymorphic microsatellite loci in the seven studied parrot taxa (Psittacidae, Aves). A, number of alleles; HO, observed heterozygosity; HE, expected heterozygosity; PIC, Polymorphism Information Content; Fis, fixation index; Pnull, probability of null alleles; Range (bp), allele range in base pairs; GenBank, GenBank Accessi...
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The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics t...
Data
Standard curves for the qPCR for Ae. albopictus, Ae. j. japonicus and Ae. koreicus. The mean cycle threshold (Ct: the cycle at which fluorescence from amplification exceeds the background fluorescence) for 10-fold serial dilutions plotted against the quantity of DNA [log10; 0 = 1 fg x ?L-1]. Coefficients of correlation (R2) were > 99.5% for all tes...
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Repeated introductions and spread of invasive mosquito species (IMS) have been recorded on a large scale these last decades worldwide. In this context, members of the mosquito genus Aedes can present serious risks to public health as they have or may develop vector competence for various viral diseases. While the Tiger mosquito (Aedes albopictus) i...
Data
Origin of target and non-target specimens used for preliminary setup and cross-amplification tests. (DOC)
Data
Results of the in silico validation of the Culicidae primers. The analysis was based on the results of an electronic PCR using ecoPCR software [48] on the EMBL-Bank release 127 (April 2016), allowing a maximum of three mismatches per primer. A) sequence logos of the forward and reverse primers illustrating the quality of the match between the prime...
Data
Number of Culicidae DNA sequences obtained by NGS before and after the filtering procedure for each sampled site, and their assignation to taxa after comparison with the local database. (XLS)
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Genetic pollution through introgressive hybridization of local species by exotic relatives is a major, yet neglected aspect of biological invasions, particularly in amphibians where human introductions are frequent. In Western Switzerland, crested newts make an interesting case: the Italian species Triturus carnifex was introduced at least a centur...
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With their direct link to individual fitness, genes of the major histocompatibility complex (MHC) are a popular system to study the evolution of adaptive genetic diversity. However, owing to the highly dynamic evolution of the MHC region the isolation, characterization, and genotyping of MHC genes remain a major challenge. While high-throughput seq...
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Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that bar...
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p>Following protection measures implemented since the 1970s, large carnivores are currently increasing in number and returning to areas from which they were absent for decades or even centuries. Monitoring programmes for these species rely extensively on non-invasive sampling and genotyping. However, attempts to connect results of such studies at l...
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Full-text available
Following protection measures implemented since the 1970s, large carnivores are currently increasing in number and returning to areas from which they were absent for decades or even centuries. Monitoring programmes for these species rely extensively on non-invasive sampling and genotyping. However, attempts to connect results of such studies at lar...
Article
Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that bar...
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Neutral and selective processes can drive repeated patterns of evolution in different groups of populations experiencing similar ecological gradients. In this paper, we used a combination of nuclear and mitochondrial DNA markers, as well as geometric morphometrics, to investigate repeated patterns of morphological and genetic divergence of European...
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Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous chall...
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The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multi...
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Coastal primary rainforests have suffered damage in Côte d'Ivoire as a result of a lack of protection and urban pressures. Consequently, the highly endemic and critically endangered Wimmer's shrew, Crocidura wimmeri, known only from its type locality, Adiopodoumé, near Abidjan, was considered to have been extinct since 1976. Shrew species assignmen...
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Host-pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driv...
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Amphibians display wide variations in life-history traits and life cycles that should prove useful to explore the evolution of sex-biased dispersal, but quantitative data on sex-specific dispersal patterns are scarce. Here, we focused on Salamandra atra, an endemic alpine species showing peculiar life-history traits. Strictly terrestrial and vivipa...
Data
Details of the results of the parentage assignment analysis with a 80% confidence threshold. (DOC)
Data
Microsatellite characterisation and genotyping. (DOC)
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Habitat restoration measures may result in artificially high breeding density, for instance when nest-boxes saturate the environment, which can negatively impact species' demography. Potential risks include changes in mating and reproductive behaviour such as increased extra-pair paternity, conspecific brood parasitism, and polygyny. Under particul...
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Avian malaria studies have taken a prominent place in different aspects of evolutionary ecology. Despite a recent interest in the role of vectors within the complex interaction system of the malaria parasite, they have largely been ignored in most epidemiological studies. Epidemiology of the disease is however strongly related to the vector's ecolo...
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Local adaptation is a major mechanism underlying the maintenance of phenotypic variation in spatially heterogeneous environments. In the barn owl (Tyto alba), dark and pale reddish-pheomelanic individuals are adapted to conditions prevailing in northern and southern Europe, respectively. Using a long-term dataset from Central Europe, we report resu...
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Natural selection drives local adaptation, potentially even at small temporal and spatial scales. As a result, adaptive genetic and phenotypic divergence can occur among populations living in different habitats. We investigated patterns of differentiation between contrasting lake and stream habitats in the cyprinid fish European minnow (Phoxinus ph...
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Parental effort is usually associated with high metabolism that could lead to an increase in the production of reactive oxidative species giving rise to oxidative stress. Since many antioxidants involved in the resistance to oxidative stress can also enhance immune function, an increase in parental effort may diminish the level of antioxidants othe...
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High-fidelity 'proofreading' polymerases are often used in library construction for next-generation sequencing projects, in an effort to minimize errors in the resulting sequence data. The increased template fidelity of these polymerases can come at the cost of reduced template specificity, and library preparation methods based on the AFLP techniqu...
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Habitat destruction and fragmentation are known to strongly affect dispersal by altering the quality of the environment between populations. As a consequence, lower landscape connectivity is expected to enhance extinction risks through a decrease in gene flow and the resulting negative effects of genetic drift, accumulation of deleterious mutations...